An upper bound on the convergence rate of a second functional in optimal sequence alignment

Hauser, Raphael and Matzinger, Heinrich and Popescu, Ionel
(2014)
An upper bound on the convergence rate of a second functional in optimal sequence alignment.
Technical Report.
Not specified.
(Submitted)

Abstract

Consider finite sequences and of
length , consisting of i.i.d.samples of random letters from a finite alphabet, and let and be chosen i.i.d.randomly from the unit ball in the space of symmetric scoring functions over this alphabet augmented by a gap symbol. We prove a probabilistic upper bound of linear order in for the deviation of the score relative to of optimal alignments with gaps of and relative to . It remains an open problem to prove a lower bound. Our result contributes to the understanding of the microstructure of
optimal alignments relative to one given scoring function, extending a theory begun in .